Submit Neuron 8.0.0 - Githubissues

biosimulators-daemon commented 3 years ago

id: neuron version: 8.0.0 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_pyNeuroML/773ee76d0b186b0e166dcda905376f14f8277ff0/biosimulators-neuron.json specificationsPatch: version: 8.0.0 image: url: ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0 validateImage: true commitSimulator: true

Changelog:

HPC connection restored

biosimulators-daemon commented 3 years ago

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!

The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.

We will discuss any concerns with your submission in this issue.

A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

biosimulators-daemon commented 3 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 3 years ago

Summary of tests

Executed 73 test cases
Passed 30 test cases:
- cli.CliDescribesSupportedEnvironmentVariablesInline
- cli.CliDisplaysHelpInline
- cli.CliDisplaysVersionInformationInline
- combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
- combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
- combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
- combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
- docker_image.DeclaresSupportedEnvironmentVariables
- docker_image.DefaultUserIsRoot
- docker_image.HasBioContainersLabels
- docker_image.HasOciLabels
- docker_image.SingularityImageExecutesSimulationsSuccessfully
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
- results_report.SimulatorGeneratesReportsOfSimulationResults
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
- sedml.SimulatorSupportsDataSetsWithDifferentShapes
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Failed 0 test cases
Skipped 43 test cases:
- published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
- published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
- published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
- published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
- published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
- published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
- published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
- published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
- published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
- published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
- published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsComputeModelChanges
- sedml.SimulatorSupportsModelAttributeChanges
- sedml.SimulatorSupportsRepeatedTasksWithChanges
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
- sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
- sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
- sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
- sedml.SimulatorSupportsSubstitutingAlgorithms
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

biosimulators-daemon commented 3 years ago

Warnings

`cli.CliDescribesSupportedEnvironmentVariablesInline` (3.4 s)

Test that the inline help for a command-line interface describes the environment variables that the simulator supports.

Warnings:

  The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

  The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
    - 'ALGORITHM_SUBSTITUTION_POLICY'
    - 'BUNDLE_OUTPUTS'
    - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
    - 'COLLECT_SED_DOCUMENT_RESULTS'
    - 'DEBUG'
    - 'H5_REPORTS_PATH'
    - 'KEEP_INDIVIDUAL_OUTPUTS'
    - 'LOG_PATH'
    - 'PLOTS_PATH'
    - 'REPORTS_PATH'
    - 'REPORT_FORMATS'
    - 'SAVE_PLOT_DATA'
    - 'VALIDATE_IMAGES'
    - 'VALIDATE_OMEX_MANIFESTS'
    - 'VALIDATE_OMEX_METADATA'
    - 'VALIDATE_RESULTS'
    - 'VALIDATE_SEDML'
    - 'VALIDATE_SEDML_MODELS'
    - 'VERBOSE'
    - 'VIZ_FORMATS'

  If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

  Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

`docker_image.DeclaresSupportedEnvironmentVariables` (0.3 s)

Test if a Docker image declares the environment variables that is supports

Warnings:

  Docker images for simulation tools should declare the environment variables that they support.

  The Docker image does not declare the following standard environment variables recognized by BioSimulators:
    - 'ALGORITHM_SUBSTITUTION_POLICY'
    - 'BUNDLE_OUTPUTS'
    - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
    - 'COLLECT_SED_DOCUMENT_RESULTS'
    - 'DEBUG'
    - 'H5_REPORTS_PATH'
    - 'KEEP_INDIVIDUAL_OUTPUTS'
    - 'LOG_PATH'
    - 'PLOTS_PATH'
    - 'REPORTS_PATH'
    - 'REPORT_FORMATS'
    - 'SAVE_PLOT_DATA'
    - 'VALIDATE_IMAGES'
    - 'VALIDATE_OMEX_MANIFESTS'
    - 'VALIDATE_OMEX_METADATA'
    - 'VALIDATE_RESULTS'
    - 'VALIDATE_SEDML'
    - 'VALIDATE_SEDML_MODELS'
    - 'VIZ_FORMATS'

  If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

  Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

`docker_image.HasBioContainersLabels` (0.3 s)

Test that a Docker image has BioContainers labels with metadata about the image

Warnings:

  The Docker image should have the following BioContainers labels:
    extra.identifiers.biotools

Log:

`published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE` (11.8 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004 Algorithm: KISAO_0000019

Warnings:

Unexpected reports were produced:
simulation.sedml/plot

Log:

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:

simulation.sedml:

  Tasks (1):

    task

  Reports (1):

    report: 5 data sets

  Plots (1):

    plot: 4 curves

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

SED documents (1):

  Succeeded: 1

  Skipped: 0

  Failed: 0

Tasks (1):

  Succeeded: 1

  Skipped: 0

  Failed: 0

Outputs (2):

  Succeeded: 2

  Skipped: 0

  Failed: 0

biosimulators-daemon commented 3 years ago

Skips

`published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ` (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3972 Algorithm: KISAO_0000263

Reason for skip:
```
Case requires model formats format_3972 and simulation algorithms KISAO_0000263
```
Log:
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_3972 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_3972 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_3240 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_3240 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_3240 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_3240 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_9004 Algorithm: KISAO_0000030

Reason for skip:
```
Case requires model formats format_9004 and simulation algorithms KISAO_0000030
```
Log:
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_9012 Algorithm: KISAO_0000669

Reason for skip:
```
Case requires model formats format_9012 and simulation algorithms KISAO_0000669
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000086

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000086
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000088

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000088
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_000019

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000496

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000496
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000560

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000560
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000560

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000560
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019
Format: format_2585 Algorithm: KISAO_0000027
Format: format_2585 Algorithm: KISAO_0000030

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027, KISAO_0000030
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000027

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000027
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000029

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000029
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000437

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000437
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000449

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000449
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000449

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000449
```
Log:
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_9001 Algorithm: KISAO_0000057

Reason for skip:
```
Case requires model formats format_9001 and simulation algorithms KISAO_0000057
```
Log:
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9010 Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log:

`sedml.SimulatorProducesLinear3DPlots` (0.8 s)

Test that a simulator produces linear 3D plots

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

`sedml.SimulatorProducesLogarithmic3DPlots` (0.8 s)

Test that a simulator produces logarithmic 3D plots

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

`sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges` (0.8 s)

Test that a simulator supports model changes that involve adding, replacing, and removing model elements.

Reason for skip:

'cython_function_or_method' object has no attribute 'rpartition'

Log:

`sedml.SimulatorSupportsAlgorithmParameters` (0.8 s)

Test that a simulator supports setting the values of parameters of algorithms

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

`sedml.SimulatorSupportsComputeModelChanges` (0.7 s)

Test that a simulator supports compute model changes

Reason for skip:

'cython_function_or_method' object has no attribute 'rpartition'

Log:

`sedml.SimulatorSupportsModelAttributeChanges` (0.7 s)

Test that a simulator supports changes to the attributes of model elements

Reason for skip:

'cython_function_or_method' object has no attribute 'rpartition'

Log:

`sedml.SimulatorSupportsRepeatedTasksWithChanges` (0.8 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

'cython_function_or_method' object has no attribute 'rpartition'

Log:

`sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables` (0.7 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables

Reason for skip:

'cython_function_or_method' object has no attribute 'rpartition'

Log:

`sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges` (8.8 s)

Test that a simulator supports repeated tasks over functional ranges

Reason for skip:

The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

Unknown error

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe SED document is potentially incorrect.

- Output `__repeated_task_report` may be invalid.

  - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe COMBINE/OMEX archive may be invalid.

- The SED-ML file at location `simulation.sedml` may be invalid.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

simulation.sedml:

  Tasks (2):

    __repeated_task_0

    task

  Reports (2):

    __repeated_task_report: 5 data sets

    task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

SED documents (1):

  Succeeded: 0

  Skipped: 0

  Failed: 1

Tasks (2):

  Succeeded: 1

  Skipped: 0

  Failed: 1

Outputs (2):

  Succeeded: 1

  Skipped: 1

  Failed: 0

[31mThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

  `pyNeuroML` was not able to execute `/tmp/tmpze28570x.xml`

    pyNeuroML >>> *** Problem running command: 

    pyNeuroML >>>        Command 'java -Xmx5752M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmp347nt1zp.xml"  -nogui -I ''' returned non-zero exit status 1.

    pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

    pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp347nt1zp.xml with jLEMS, NO GUI mode...

    pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

    pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpouedmbqa, /tmp, /tmp, /tmp/tmpouedmbqa]

    pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

    pyNeuroML >>>  jNeuroML >>  

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 20:11  (INFO) Loading LEMS file from: /tmp/tmp347nt1zp.xml

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 20:11  (INFO) Reading from: /tmp/tmp347nt1zp.xml

    pyNeuroML >>>  jNeuroML >>  

    [0m

`sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges` (8.6 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:

The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

Unknown error

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe SED document is potentially incorrect.

- Output `__repeated_task_report` may be invalid.

  - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe COMBINE/OMEX archive may be invalid.

- The SED-ML file at location `simulation.sedml` may be invalid.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

simulation.sedml:

  Tasks (2):

    __repeated_task_0

    task

  Reports (2):

    __repeated_task_report: 5 data sets

    task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

SED documents (1):

  Succeeded: 0

  Skipped: 0

  Failed: 1

Tasks (2):

  Succeeded: 1

  Skipped: 0

  Failed: 1

Outputs (2):

  Succeeded: 1

  Skipped: 1

  Failed: 0

[31mThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

  `pyNeuroML` was not able to execute `/tmp/tmpzicud78e.xml`

    pyNeuroML >>> *** Problem running command: 

    pyNeuroML >>>        Command 'java -Xmx5752M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmp3gz_2q0b.xml"  -nogui -I ''' returned non-zero exit status 1.

    pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

    pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp3gz_2q0b.xml with jLEMS, NO GUI mode...

    pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

    pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmptglpjvv_, /tmp, /tmp, /tmp/tmptglpjvv_]

    pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

    pyNeuroML >>>  jNeuroML >>  

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 20:11  (INFO) Loading LEMS file from: /tmp/tmp3gz_2q0b.xml

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 20:11  (INFO) Reading from: /tmp/tmp3gz_2q0b.xml

    pyNeuroML >>>  jNeuroML >>  

    [0m

`sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges` (8.8 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:

The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

Unknown error

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe SED document is potentially incorrect.

- Output `__repeated_task_report` may be invalid.

  - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe COMBINE/OMEX archive may be invalid.

- The SED-ML file at location `simulation.sedml` may be invalid.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

simulation.sedml:

  Tasks (2):

    __repeated_task_0

    task

  Reports (2):

    __repeated_task_report: 5 data sets

    task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

SED documents (1):

  Succeeded: 0

  Skipped: 0

  Failed: 1

Tasks (2):

  Succeeded: 1

  Skipped: 0

  Failed: 1

Outputs (2):

  Succeeded: 1

  Skipped: 1

  Failed: 0

[31mThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

  `pyNeuroML` was not able to execute `/tmp/tmpqknn3z7t.xml`

    pyNeuroML >>> *** Problem running command: 

    pyNeuroML >>>        Command 'java -Xmx5747M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpt4_9t3gu.xml"  -nogui -I ''' returned non-zero exit status 1.

    pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

    pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpt4_9t3gu.xml with jLEMS, NO GUI mode...

    pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

    pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpo289ugrk, /tmp, /tmp, /tmp/tmpo289ugrk]

    pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

    pyNeuroML >>>  jNeuroML >>  

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 20:11  (INFO) Loading LEMS file from: /tmp/tmpt4_9t3gu.xml

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 20:11  (INFO) Reading from: /tmp/tmpt4_9t3gu.xml

    pyNeuroML >>>  jNeuroML >>  

    [0m

`sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks` (8.6 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

Unknown error

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe SED document is potentially incorrect.

- Output `__repeated_task_report` may be invalid.

  - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe COMBINE/OMEX archive may be invalid.

- The SED-ML file at location `simulation.sedml` may be invalid.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

simulation.sedml:

  Tasks (2):

    __repeated_task_0

    task

  Reports (2):

    __repeated_task_report: 5 data sets

    task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

SED documents (1):

  Succeeded: 0

  Skipped: 0

  Failed: 1

Tasks (2):

  Succeeded: 1

  Skipped: 0

  Failed: 1

Outputs (2):

  Succeeded: 1

  Skipped: 1

  Failed: 0

[31mThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

  `pyNeuroML` was not able to execute `/tmp/tmp1n35275k.xml`

    pyNeuroML >>> *** Problem running command: 

    pyNeuroML >>>        Command 'java -Xmx5746M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmp0sio1ddj.xml"  -nogui -I ''' returned non-zero exit status 1.

    pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

    pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp0sio1ddj.xml with jLEMS, NO GUI mode...

    pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

    pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmp8wze1_ht, /tmp, /tmp, /tmp/tmp8wze1_ht]

    pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

    pyNeuroML >>>  jNeuroML >>  

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 20:11  (INFO) Loading LEMS file from: /tmp/tmp0sio1ddj.xml

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 20:11  (INFO) Reading from: /tmp/tmp0sio1ddj.xml

    pyNeuroML >>>  jNeuroML >>  

    [0m

`sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges` (8.7 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables

Reason for skip:

The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

Unknown error

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe SED document is potentially incorrect.

- Output `__repeated_task_report` may be invalid.

  - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe COMBINE/OMEX archive may be invalid.

- The SED-ML file at location `simulation.sedml` may be invalid.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

simulation.sedml:

  Tasks (2):

    __repeated_task_0

    task

  Reports (2):

    __repeated_task_report: 5 data sets

    task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

SED documents (1):

  Succeeded: 0

  Skipped: 0

  Failed: 1

Tasks (2):

  Succeeded: 1

  Skipped: 0

  Failed: 1

Outputs (2):

  Succeeded: 1

  Skipped: 1

  Failed: 0

[31mThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

  `pyNeuroML` was not able to execute `/tmp/tmppyrvp4ij.xml`

    pyNeuroML >>> *** Problem running command: 

    pyNeuroML >>>        Command 'java -Xmx5746M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpjtojcave.xml"  -nogui -I ''' returned non-zero exit status 1.

    pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

    pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpjtojcave.xml with jLEMS, NO GUI mode...

    pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

    pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmp7e76vrn2, /tmp, /tmp, /tmp/tmp7e76vrn2]

    pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

    pyNeuroML >>>  jNeuroML >>  

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 20:12  (INFO) Loading LEMS file from: /tmp/tmpjtojcave.xml

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 20:12  (INFO) Reading from: /tmp/tmpjtojcave.xml

    pyNeuroML >>>  jNeuroML >>  

    [0m

`sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks` (9.4 s)

Test that a simulator supports nested repeated tasks

Reason for skip:

The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

Unknown error

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe SED document is potentially incorrect.

- Output `__repeated_task_report` may be invalid.

  - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe COMBINE/OMEX archive may be invalid.

- The SED-ML file at location `simulation.sedml` may be invalid.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 3 tasks, 2 reports, and 0 plots:

simulation.sedml:

  Tasks (3):

    __repeated_task_0

    __repeated_task_1

    task

  Reports (2):

    __repeated_task_report: 5 data sets

    task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

SED documents (1):

  Succeeded: 0

  Skipped: 0

  Failed: 1

Tasks (3):

  Succeeded: 1

  Skipped: 0

  Failed: 2

Outputs (2):

  Succeeded: 1

  Skipped: 1

  Failed: 0

[31mThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

  `pyNeuroML` was not able to execute `/tmp/tmp5ew3rpb0.xml`

    pyNeuroML >>> *** Problem running command: 

    pyNeuroML >>>        Command 'java -Xmx5741M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmp33w4_2zw.xml"  -nogui -I ''' returned non-zero exit status 1.

    pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

    pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp33w4_2zw.xml with jLEMS, NO GUI mode...

    pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

    pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpl5fcu9ky, /tmp, /tmp, /tmp/tmpl5fcu9ky]

    pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

    pyNeuroML >>>  jNeuroML >>  

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 20:12  (INFO) Loading LEMS file from: /tmp/tmp33w4_2zw.xml

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 20:12  (INFO) Reading from: /tmp/tmp33w4_2zw.xml

    pyNeuroML >>>  jNeuroML >>  

  `pyNeuroML` was not able to execute `/tmp/tmp9xb_v93t.xml`

    pyNeuroML >>> *** Problem running command: 

    pyNeuroML >>>        Command 'java -Xmx5741M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmp69w6xf6i.xml"  -nogui -I ''' returned non-zero exit status 1.

    pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

    pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp69w6xf6i.xml with jLEMS, NO GUI mode...

    pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

    pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpmaestcll, /tmp, /tmp, /tmp/tmpmaestcll]

    pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

    pyNeuroML >>>  jNeuroML >>  

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 20:12  (INFO) Loading LEMS file from: /tmp/tmp69w6xf6i.xml

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 20:12  (INFO) Reading from: /tmp/tmp69w6xf6i.xml

    pyNeuroML >>>  jNeuroML >>  

    [0m

`sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes` (9.3 s)

Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their order attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes.

Reason for skip:

The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

Unknown error

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe SED document is potentially incorrect.

- Task `__repeated_task_1` may be invalid.

  - The outputs of the sub-tasks have different shapes.

- Output `__repeated_task_report` may be invalid.

  - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe COMBINE/OMEX archive may be invalid.

- The SED-ML file at location `simulation.sedml` may be invalid.

  - Task `__repeated_task_1` may be invalid.

    - The outputs of the sub-tasks have different shapes.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 3 tasks, 2 reports, and 0 plots:

simulation.sedml:

  Tasks (3):

    __repeated_task_0

    __repeated_task_1

    task

  Reports (2):

    __repeated_task_report: 5 data sets

    task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

SED documents (1):

  Succeeded: 0

  Skipped: 0

  Failed: 1

Tasks (3):

  Succeeded: 1

  Skipped: 0

  Failed: 2

Outputs (2):

  Succeeded: 1

  Skipped: 1

  Failed: 0

[31mThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

  `pyNeuroML` was not able to execute `/tmp/tmpcilyst4p.xml`

    pyNeuroML >>> *** Problem running command: 

    pyNeuroML >>>        Command 'java -Xmx5744M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmp7oed61l7.xml"  -nogui -I ''' returned non-zero exit status 1.

    pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

    pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp7oed61l7.xml with jLEMS, NO GUI mode...

    pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

    pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmppoyc1u9t, /tmp, /tmp, /tmp/tmppoyc1u9t]

    pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

    pyNeuroML >>>  jNeuroML >>  

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 20:12  (INFO) Loading LEMS file from: /tmp/tmp7oed61l7.xml

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 20:12  (INFO) Reading from: /tmp/tmp7oed61l7.xml

    pyNeuroML >>>  jNeuroML >>  

  `pyNeuroML` was not able to execute `/tmp/tmpwzc_gqz4.xml`

    pyNeuroML >>> *** Problem running command: 

    pyNeuroML >>>        Command 'java -Xmx5744M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmp0zg0f5r6.xml"  -nogui -I ''' returned non-zero exit status 1.

    pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

    pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp0zg0f5r6.xml with jLEMS, NO GUI mode...

    pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

    pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpv3dl4ey6, /tmp, /tmp, /tmp/tmpv3dl4ey6]

    pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

    pyNeuroML >>>  jNeuroML >>  

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 20:12  (INFO) Loading LEMS file from: /tmp/tmp0zg0f5r6.xml

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 20:12  (INFO) Reading from: /tmp/tmp0zg0f5r6.xml

    pyNeuroML >>>  jNeuroML >>  

    [0m

`sedml.SimulatorSupportsRepeatedTasksWithVectorRanges` (8.6 s)

Test that a simulator supports repeated tasks over vector ranges

Reason for skip:

The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

Unknown error

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe SED document is potentially incorrect.

- Output `__repeated_task_report` may be invalid.

  - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe COMBINE/OMEX archive may be invalid.

- The SED-ML file at location `simulation.sedml` may be invalid.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

simulation.sedml:

  Tasks (2):

    __repeated_task_0

    task

  Reports (2):

    __repeated_task_report: 5 data sets

    task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

SED documents (1):

  Succeeded: 0

  Skipped: 0

  Failed: 1

Tasks (2):

  Succeeded: 1

  Skipped: 0

  Failed: 1

Outputs (2):

  Succeeded: 1

  Skipped: 1

  Failed: 0

[31mThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

  `pyNeuroML` was not able to execute `/tmp/tmpukaooeo0.xml`

    pyNeuroML >>> *** Problem running command: 

    pyNeuroML >>>        Command 'java -Xmx5748M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpqwtx_gyw.xml"  -nogui -I ''' returned non-zero exit status 1.

    pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

    pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpqwtx_gyw.xml with jLEMS, NO GUI mode...

    pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

    pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpha0ogr16, /tmp, /tmp, /tmp/tmpha0ogr16]

    pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

    pyNeuroML >>>  jNeuroML >>  

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 20:12  (INFO) Loading LEMS file from: /tmp/tmpqwtx_gyw.xml

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 20:12  (INFO) Reading from: /tmp/tmpqwtx_gyw.xml

    pyNeuroML >>>  jNeuroML >>  

    [0m

`sedml.SimulatorSupportsSubstitutingAlgorithms` (26.4 s)

Check that a simulator can substitute algorithms that it doesn't implement with similar algorithms when the algorithm substitution policy is less restrictive than :obj:AlgorithmSubstitutionPolicy.SAME_METHOD. Also check that a simulator ignores unsupported algorithm parameters when the algorithm substitution policy is less restrictive than :obj:AlgorithmSubstitutionPolicy.NONE.

Reason for skip:

The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

Unknown error

Log:


Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

simulation.sedml:

  Tasks (1):

    task

  Reports (1):

    report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

SED documents (1):

  Succeeded: 0

  Skipped: 0

  Failed: 1

Tasks (1):

  Succeeded: 0

  Skipped: 0

  Failed: 1

Outputs (1):

  Succeeded: 0

  Skipped: 1

  Failed: 0

[31mThe COMBINE/OMEX did not exe ...

biosimulators-daemon commented 3 years ago

The image for your simulator is valid!

biosimulators-daemon commented 3 years ago

The validation/submission of your simulator failed.

- A Singularity image could not be generated for the Docker image
- 
-   - Internal Server Error (500):

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

biosimulators-daemon commented 3 years ago

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!

The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.

We will discuss any concerns with your submission in this issue.

A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

biosimulators-daemon commented 3 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 3 years ago

Summary of tests

Executed 73 test cases
Passed 30 test cases:
- cli.CliDescribesSupportedEnvironmentVariablesInline
- cli.CliDisplaysHelpInline
- cli.CliDisplaysVersionInformationInline
- combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
- combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
- combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
- combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
- docker_image.DeclaresSupportedEnvironmentVariables
- docker_image.DefaultUserIsRoot
- docker_image.HasBioContainersLabels
- docker_image.HasOciLabels
- docker_image.SingularityImageExecutesSimulationsSuccessfully
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
- results_report.SimulatorGeneratesReportsOfSimulationResults
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
- sedml.SimulatorSupportsDataSetsWithDifferentShapes
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Failed 0 test cases
Skipped 43 test cases:
- published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
- published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
- published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
- published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
- published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
- published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
- published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
- published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
- published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
- published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
- published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsComputeModelChanges
- sedml.SimulatorSupportsModelAttributeChanges
- sedml.SimulatorSupportsRepeatedTasksWithChanges
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
- sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
- sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
- sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
- sedml.SimulatorSupportsSubstitutingAlgorithms
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

biosimulators-daemon commented 3 years ago

Warnings

`cli.CliDescribesSupportedEnvironmentVariablesInline` (3.4 s)

Test that the inline help for a command-line interface describes the environment variables that the simulator supports.

Warnings:

  The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

  The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
    - 'ALGORITHM_SUBSTITUTION_POLICY'
    - 'BUNDLE_OUTPUTS'
    - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
    - 'COLLECT_SED_DOCUMENT_RESULTS'
    - 'DEBUG'
    - 'H5_REPORTS_PATH'
    - 'KEEP_INDIVIDUAL_OUTPUTS'
    - 'LOG_PATH'
    - 'PLOTS_PATH'
    - 'REPORTS_PATH'
    - 'REPORT_FORMATS'
    - 'SAVE_PLOT_DATA'
    - 'VALIDATE_IMAGES'
    - 'VALIDATE_OMEX_MANIFESTS'
    - 'VALIDATE_OMEX_METADATA'
    - 'VALIDATE_RESULTS'
    - 'VALIDATE_SEDML'
    - 'VALIDATE_SEDML_MODELS'
    - 'VERBOSE'
    - 'VIZ_FORMATS'

  If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

  Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

`docker_image.DeclaresSupportedEnvironmentVariables` (0.3 s)

Test if a Docker image declares the environment variables that is supports

Warnings:

  Docker images for simulation tools should declare the environment variables that they support.

  The Docker image does not declare the following standard environment variables recognized by BioSimulators:
    - 'ALGORITHM_SUBSTITUTION_POLICY'
    - 'BUNDLE_OUTPUTS'
    - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
    - 'COLLECT_SED_DOCUMENT_RESULTS'
    - 'DEBUG'
    - 'H5_REPORTS_PATH'
    - 'KEEP_INDIVIDUAL_OUTPUTS'
    - 'LOG_PATH'
    - 'PLOTS_PATH'
    - 'REPORTS_PATH'
    - 'REPORT_FORMATS'
    - 'SAVE_PLOT_DATA'
    - 'VALIDATE_IMAGES'
    - 'VALIDATE_OMEX_MANIFESTS'
    - 'VALIDATE_OMEX_METADATA'
    - 'VALIDATE_RESULTS'
    - 'VALIDATE_SEDML'
    - 'VALIDATE_SEDML_MODELS'
    - 'VIZ_FORMATS'

  If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

  Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

`docker_image.HasBioContainersLabels` (0.2 s)

Test that a Docker image has BioContainers labels with metadata about the image

Warnings:

  The Docker image should have the following BioContainers labels:
    extra.identifiers.biotools

Log:

`published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE` (11.7 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004 Algorithm: KISAO_0000019

Warnings:

Unexpected reports were produced:
simulation.sedml/plot

Log:

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:

simulation.sedml:

  Tasks (1):

    task

  Reports (1):

    report: 5 data sets

  Plots (1):

    plot: 4 curves

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

SED documents (1):

  Succeeded: 1

  Skipped: 0

  Failed: 0

Tasks (1):

  Succeeded: 1

  Skipped: 0

  Failed: 0

Outputs (2):

  Succeeded: 2

  Skipped: 0

  Failed: 0

biosimulators-daemon commented 3 years ago

Skips

`published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ` (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_3972 Algorithm: KISAO_0000263

Reason for skip:
```
Case requires model formats format_3972 and simulation algorithms KISAO_0000263
```
Log:
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_3972 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_3972 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_3240 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_3240 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_3240 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_3240 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_9004 Algorithm: KISAO_0000030

Reason for skip:
```
Case requires model formats format_9004 and simulation algorithms KISAO_0000030
```
Log:
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_9012 Algorithm: KISAO_0000669

Reason for skip:
```
Case requires model formats format_9012 and simulation algorithms KISAO_0000669
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000086

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000086
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000088

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000088
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_000019

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000496

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000496
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000560

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000560
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000560

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000560
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019
Format: format_2585 Algorithm: KISAO_0000027
Format: format_2585 Algorithm: KISAO_0000030

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027, KISAO_0000030
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000019

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000019
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000027

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000027
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000029

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000029
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000437

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000437
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000449

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000449
```
Log:
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_2585 Algorithm: KISAO_0000449

Reason for skip:
```
Case requires model formats format_2585 and simulation algorithms KISAO_0000449
```
Log:
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)

Required model formats and simulation algorithms for SED tasks:
Format: format_9001 Algorithm: KISAO_0000057

Reason for skip:
```
Case requires model formats format_9001 and simulation algorithms KISAO_0000057
```
Log:
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9010 Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log:

`sedml.SimulatorProducesLinear3DPlots` (0.8 s)

Test that a simulator produces linear 3D plots

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

`sedml.SimulatorProducesLogarithmic3DPlots` (0.8 s)

Test that a simulator produces logarithmic 3D plots

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

`sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges` (0.8 s)

Test that a simulator supports model changes that involve adding, replacing, and removing model elements.

Reason for skip:

'cython_function_or_method' object has no attribute 'rpartition'

Log:

`sedml.SimulatorSupportsAlgorithmParameters` (0.8 s)

Test that a simulator supports setting the values of parameters of algorithms

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

`sedml.SimulatorSupportsComputeModelChanges` (0.6 s)

Test that a simulator supports compute model changes

Reason for skip:

'cython_function_or_method' object has no attribute 'rpartition'

Log:

`sedml.SimulatorSupportsModelAttributeChanges` (0.7 s)

Test that a simulator supports changes to the attributes of model elements

Reason for skip:

'cython_function_or_method' object has no attribute 'rpartition'

Log:

`sedml.SimulatorSupportsRepeatedTasksWithChanges` (1.3 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

'cython_function_or_method' object has no attribute 'rpartition'

Log:

`sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables` (0.7 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables

Reason for skip:

'cython_function_or_method' object has no attribute 'rpartition'

Log:

`sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges` (8.8 s)

Test that a simulator supports repeated tasks over functional ranges

Reason for skip:

The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

Unknown error

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe SED document is potentially incorrect.

- Output `__repeated_task_report` may be invalid.

  - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe COMBINE/OMEX archive may be invalid.

- The SED-ML file at location `simulation.sedml` may be invalid.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

simulation.sedml:

  Tasks (2):

    __repeated_task_0

    task

  Reports (2):

    __repeated_task_report: 5 data sets

    task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

SED documents (1):

  Succeeded: 0

  Skipped: 0

  Failed: 1

Tasks (2):

  Succeeded: 1

  Skipped: 0

  Failed: 1

Outputs (2):

  Succeeded: 1

  Skipped: 1

  Failed: 0

[31mThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

  `pyNeuroML` was not able to execute `/tmp/tmpmrsewd1a.xml`

    pyNeuroML >>> *** Problem running command: 

    pyNeuroML >>>        Command 'java -Xmx5738M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmp5f8eq52s.xml"  -nogui -I ''' returned non-zero exit status 1.

    pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

    pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp5f8eq52s.xml with jLEMS, NO GUI mode...

    pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

    pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpbu2bzdoh, /tmp, /tmp, /tmp/tmpbu2bzdoh]

    pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

    pyNeuroML >>>  jNeuroML >>  

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 23:56  (INFO) Loading LEMS file from: /tmp/tmp5f8eq52s.xml

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 23:56  (INFO) Reading from: /tmp/tmp5f8eq52s.xml

    pyNeuroML >>>  jNeuroML >>  

    [0m

`sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges` (8.5 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:

The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

Unknown error

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe SED document is potentially incorrect.

- Output `__repeated_task_report` may be invalid.

  - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe COMBINE/OMEX archive may be invalid.

- The SED-ML file at location `simulation.sedml` may be invalid.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

simulation.sedml:

  Tasks (2):

    __repeated_task_0

    task

  Reports (2):

    __repeated_task_report: 5 data sets

    task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

SED documents (1):

  Succeeded: 0

  Skipped: 0

  Failed: 1

Tasks (2):

  Succeeded: 1

  Skipped: 0

  Failed: 1

Outputs (2):

  Succeeded: 1

  Skipped: 1

  Failed: 0

[31mThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

  `pyNeuroML` was not able to execute `/tmp/tmp65dggrw6.xml`

    pyNeuroML >>> *** Problem running command: 

    pyNeuroML >>>        Command 'java -Xmx5739M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpkqy_1cq2.xml"  -nogui -I ''' returned non-zero exit status 1.

    pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

    pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpkqy_1cq2.xml with jLEMS, NO GUI mode...

    pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

    pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpoqnp0j54, /tmp, /tmp, /tmp/tmpoqnp0j54]

    pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

    pyNeuroML >>>  jNeuroML >>  

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 23:56  (INFO) Loading LEMS file from: /tmp/tmpkqy_1cq2.xml

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 23:56  (INFO) Reading from: /tmp/tmpkqy_1cq2.xml

    pyNeuroML >>>  jNeuroML >>  

    [0m

`sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges` (8.5 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:

The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

Unknown error

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe SED document is potentially incorrect.

- Output `__repeated_task_report` may be invalid.

  - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe COMBINE/OMEX archive may be invalid.

- The SED-ML file at location `simulation.sedml` may be invalid.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

simulation.sedml:

  Tasks (2):

    __repeated_task_0

    task

  Reports (2):

    __repeated_task_report: 5 data sets

    task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

SED documents (1):

  Succeeded: 0

  Skipped: 0

  Failed: 1

Tasks (2):

  Succeeded: 1

  Skipped: 0

  Failed: 1

Outputs (2):

  Succeeded: 1

  Skipped: 1

  Failed: 0

[31mThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

  `pyNeuroML` was not able to execute `/tmp/tmpjxrydw5w.xml`

    pyNeuroML >>> *** Problem running command: 

    pyNeuroML >>>        Command 'java -Xmx5737M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmp9ecacwsy.xml"  -nogui -I ''' returned non-zero exit status 1.

    pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

    pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp9ecacwsy.xml with jLEMS, NO GUI mode...

    pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

    pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpeqfscm8z, /tmp, /tmp, /tmp/tmpeqfscm8z]

    pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

    pyNeuroML >>>  jNeuroML >>  

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 23:56  (INFO) Loading LEMS file from: /tmp/tmp9ecacwsy.xml

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 23:56  (INFO) Reading from: /tmp/tmp9ecacwsy.xml

    pyNeuroML >>>  jNeuroML >>  

    [0m

`sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks` (8.7 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

Unknown error

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe SED document is potentially incorrect.

- Output `__repeated_task_report` may be invalid.

  - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe COMBINE/OMEX archive may be invalid.

- The SED-ML file at location `simulation.sedml` may be invalid.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

simulation.sedml:

  Tasks (2):

    __repeated_task_0

    task

  Reports (2):

    __repeated_task_report: 5 data sets

    task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

SED documents (1):

  Succeeded: 0

  Skipped: 0

  Failed: 1

Tasks (2):

  Succeeded: 1

  Skipped: 0

  Failed: 1

Outputs (2):

  Succeeded: 1

  Skipped: 1

  Failed: 0

[31mThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

  `pyNeuroML` was not able to execute `/tmp/tmpe2ba1zi1.xml`

    pyNeuroML >>> *** Problem running command: 

    pyNeuroML >>>        Command 'java -Xmx5736M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpiaxjm7pr.xml"  -nogui -I ''' returned non-zero exit status 1.

    pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

    pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpiaxjm7pr.xml with jLEMS, NO GUI mode...

    pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

    pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmp7isb076h, /tmp, /tmp, /tmp/tmp7isb076h]

    pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

    pyNeuroML >>>  jNeuroML >>  

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 23:56  (INFO) Loading LEMS file from: /tmp/tmpiaxjm7pr.xml

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 23:56  (INFO) Reading from: /tmp/tmpiaxjm7pr.xml

    pyNeuroML >>>  jNeuroML >>  

    [0m

`sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges` (8.9 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables

Reason for skip:

The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

Unknown error

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe SED document is potentially incorrect.

- Output `__repeated_task_report` may be invalid.

  - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe COMBINE/OMEX archive may be invalid.

- The SED-ML file at location `simulation.sedml` may be invalid.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

simulation.sedml:

  Tasks (2):

    __repeated_task_0

    task

  Reports (2):

    __repeated_task_report: 5 data sets

    task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

SED documents (1):

  Succeeded: 0

  Skipped: 0

  Failed: 1

Tasks (2):

  Succeeded: 1

  Skipped: 0

  Failed: 1

Outputs (2):

  Succeeded: 1

  Skipped: 1

  Failed: 0

[31mThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

  `pyNeuroML` was not able to execute `/tmp/tmpl2a71ia7.xml`

    pyNeuroML >>> *** Problem running command: 

    pyNeuroML >>>        Command 'java -Xmx5727M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmp1jewo9pk.xml"  -nogui -I ''' returned non-zero exit status 1.

    pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

    pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp1jewo9pk.xml with jLEMS, NO GUI mode...

    pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

    pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpiqj6qu43, /tmp, /tmp, /tmp/tmpiqj6qu43]

    pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

    pyNeuroML >>>  jNeuroML >>  

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 23:57  (INFO) Loading LEMS file from: /tmp/tmp1jewo9pk.xml

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 23:57  (INFO) Reading from: /tmp/tmp1jewo9pk.xml

    pyNeuroML >>>  jNeuroML >>  

    [0m

`sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks` (9.2 s)

Test that a simulator supports nested repeated tasks

Reason for skip:

The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

Unknown error

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe SED document is potentially incorrect.

- Output `__repeated_task_report` may be invalid.

  - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe COMBINE/OMEX archive may be invalid.

- The SED-ML file at location `simulation.sedml` may be invalid.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 3 tasks, 2 reports, and 0 plots:

simulation.sedml:

  Tasks (3):

    __repeated_task_0

    __repeated_task_1

    task

  Reports (2):

    __repeated_task_report: 5 data sets

    task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

SED documents (1):

  Succeeded: 0

  Skipped: 0

  Failed: 1

Tasks (3):

  Succeeded: 1

  Skipped: 0

  Failed: 2

Outputs (2):

  Succeeded: 1

  Skipped: 1

  Failed: 0

[31mThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

  `pyNeuroML` was not able to execute `/tmp/tmp6gj0vh_b.xml`

    pyNeuroML >>> *** Problem running command: 

    pyNeuroML >>>        Command 'java -Xmx5730M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpedrsq8wd.xml"  -nogui -I ''' returned non-zero exit status 1.

    pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

    pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpedrsq8wd.xml with jLEMS, NO GUI mode...

    pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

    pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpz_p2mguc, /tmp, /tmp, /tmp/tmpz_p2mguc]

    pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

    pyNeuroML >>>  jNeuroML >>  

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 23:57  (INFO) Loading LEMS file from: /tmp/tmpedrsq8wd.xml

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 23:57  (INFO) Reading from: /tmp/tmpedrsq8wd.xml

    pyNeuroML >>>  jNeuroML >>  

  `pyNeuroML` was not able to execute `/tmp/tmp1hjfbtt2.xml`

    pyNeuroML >>> *** Problem running command: 

    pyNeuroML >>>        Command 'java -Xmx5730M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmp_sg6itl7.xml"  -nogui -I ''' returned non-zero exit status 1.

    pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

    pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp_sg6itl7.xml with jLEMS, NO GUI mode...

    pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

    pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpwr8m4vyb, /tmp, /tmp, /tmp/tmpwr8m4vyb]

    pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

    pyNeuroML >>>  jNeuroML >>  

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 23:57  (INFO) Loading LEMS file from: /tmp/tmp_sg6itl7.xml

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 23:57  (INFO) Reading from: /tmp/tmp_sg6itl7.xml

    pyNeuroML >>>  jNeuroML >>  

    [0m

`sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes` (9.2 s)

Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their order attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes.

Reason for skip:

The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

Unknown error

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe SED document is potentially incorrect.

- Task `__repeated_task_1` may be invalid.

  - The outputs of the sub-tasks have different shapes.

- Output `__repeated_task_report` may be invalid.

  - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe COMBINE/OMEX archive may be invalid.

- The SED-ML file at location `simulation.sedml` may be invalid.

  - Task `__repeated_task_1` may be invalid.

    - The outputs of the sub-tasks have different shapes.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 3 tasks, 2 reports, and 0 plots:

simulation.sedml:

  Tasks (3):

    __repeated_task_0

    __repeated_task_1

    task

  Reports (2):

    __repeated_task_report: 5 data sets

    task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

SED documents (1):

  Succeeded: 0

  Skipped: 0

  Failed: 1

Tasks (3):

  Succeeded: 1

  Skipped: 0

  Failed: 2

Outputs (2):

  Succeeded: 1

  Skipped: 1

  Failed: 0

[31mThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

  `pyNeuroML` was not able to execute `/tmp/tmpbqutbrdd.xml`

    pyNeuroML >>> *** Problem running command: 

    pyNeuroML >>>        Command 'java -Xmx5729M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmpowzu1e6n.xml"  -nogui -I ''' returned non-zero exit status 1.

    pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

    pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmpowzu1e6n.xml with jLEMS, NO GUI mode...

    pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

    pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpb9qtg34v, /tmp, /tmp, /tmp/tmpb9qtg34v]

    pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

    pyNeuroML >>>  jNeuroML >>  

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 23:57  (INFO) Loading LEMS file from: /tmp/tmpowzu1e6n.xml

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 23:57  (INFO) Reading from: /tmp/tmpowzu1e6n.xml

    pyNeuroML >>>  jNeuroML >>  

  `pyNeuroML` was not able to execute `/tmp/tmppo6hnkll.xml`

    pyNeuroML >>> *** Problem running command: 

    pyNeuroML >>>        Command 'java -Xmx5729M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmp8dnh1t4b.xml"  -nogui -I ''' returned non-zero exit status 1.

    pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

    pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmp8dnh1t4b.xml with jLEMS, NO GUI mode...

    pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

    pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmp4ttj2_aa, /tmp, /tmp, /tmp/tmp4ttj2_aa]

    pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

    pyNeuroML >>>  jNeuroML >>  

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 23:57  (INFO) Loading LEMS file from: /tmp/tmp8dnh1t4b.xml

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 23:57  (INFO) Reading from: /tmp/tmp8dnh1t4b.xml

    pyNeuroML >>>  jNeuroML >>  

    [0m

`sedml.SimulatorSupportsRepeatedTasksWithVectorRanges` (8.3 s)

Test that a simulator supports repeated tasks over vector ranges

Reason for skip:

The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

Unknown error

Log:

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe SED document is potentially incorrect.

- Output `__repeated_task_report` may be invalid.

  - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe COMBINE/OMEX archive may be invalid.

- The SED-ML file at location `simulation.sedml` may be invalid.

  - Output `__repeated_task_report` may be invalid.

    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m

warnings.warn(termcolor.colored(message, Colors.warning.value), category)

Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 2 reports, and 0 plots:

simulation.sedml:

  Tasks (2):

    __repeated_task_0

    task

  Reports (2):

    __repeated_task_report: 5 data sets

    task_report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

SED documents (1):

  Succeeded: 0

  Skipped: 0

  Failed: 1

Tasks (2):

  Succeeded: 1

  Skipped: 0

  Failed: 1

Outputs (2):

  Succeeded: 1

  Skipped: 1

  Failed: 0

[31mThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

  `pyNeuroML` was not able to execute `/tmp/tmpueqldbwb.xml`

    pyNeuroML >>> *** Problem running command: 

    pyNeuroML >>>        Command 'java -Xmx5728M  -Djava.awt.headless=true -jar  "/usr/local/lib/python3.9/site-packages/pyneuroml/lib/jNeuroML-0.10.3-jar-with-dependencies.jar"  "/tmp/tmppzi5vk93.xml"  -nogui -I ''' returned non-zero exit status 1.

    pyNeuroML >>>  jNeuroML >>   jNeuroML v0.10.3

    pyNeuroML >>>  jNeuroML >>  Loading: /tmp/tmppzi5vk93.xml with jLEMS, NO GUI mode...

    pyNeuroML >>>  jNeuroML >>  org.lemsml.jlems.core.sim.ContentError: Can't find file at path: NaConductance.channel.nml

    pyNeuroML >>>  jNeuroML >>  Search directories are: [/tmp/tmpcuzkk977, /tmp, /tmp, /tmp/tmpcuzkk977]

    pyNeuroML >>>  jNeuroML >>  Search paths in jar are: [/NeuroML2CoreTypes]

    pyNeuroML >>>  jNeuroML >>  

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.io.reader.JarResourceInclusionReader.getRelativeContent(JarResourceInclusionReader.java:179)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.getRelativeContent(NeuroMLInclusionReader.java:61)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.getIncludeContent(AbstractInclusionReader.java:41)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.insertIncludes(AbstractInclusionReader.java:71)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.NeuroMLInclusionReader.insertIncludes(NeuroMLInclusionReader.java:102)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.core.sim.AbstractInclusionReader.read(AbstractInclusionReader.java:24)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:259)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.readLemsNeuroMLFile(Utils.java:245)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils$1.importFile(Utils.java:505)

    pyNeuroML >>>  jNeuroML >>      at org.lemsml.jlems.viz.datadisplay.ControlPanel.initialise(ControlPanel.java:134)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:516)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493)

    pyNeuroML >>>  jNeuroML >>      at org.neuroml.JNeuroML.main(JNeuroML.java:595)

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 23:57  (INFO) Loading LEMS file from: /tmp/tmppzi5vk93.xml

    pyNeuroML >>>  jNeuroML >>  INFO Sep 01,2021 23:57  (INFO) Reading from: /tmp/tmppzi5vk93.xml

    pyNeuroML >>>  jNeuroML >>  

    [0m

`sedml.SimulatorSupportsSubstitutingAlgorithms` (26.6 s)

Check that a simulator can substitute algorithms that it doesn't implement with similar algorithms when the algorithm substitution policy is less restrictive than :obj:AlgorithmSubstitutionPolicy.SAME_METHOD. Also check that a simulator ignores unsupported algorithm parameters when the algorithm substitution policy is less restrictive than :obj:AlgorithmSubstitutionPolicy.NONE.

Reason for skip:

The image 'ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:8.0.0' could not execute the archive:

Unknown error

Log:


Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:

simulation.sedml:

  Tasks (1):

    task

  Reports (1):

    report: 5 data sets

Executing SED-ML file 0: simulation.sedml ...

Bundling outputs ...

Cleaning up ...

============= SUMMARY =============

Executed 1 SED documents:

SED documents (1):

  Succeeded: 0

  Skipped: 0

  Failed: 1

Tasks (1):

  Succeeded: 0

  Skipped: 0

  Failed: 1

Outputs (1):

  Succeeded: 0

  Skipped: 1

  Failed: 0

[31mThe COMBINE/OMEX did not exe ...

biosimulators-daemon commented 3 years ago

The image for your simulator is valid!

biosimulators-daemon commented 3 years ago

Your submission was committed to the BioSimulators registry. Thank you!

Future submissions of subsequent versions of neuron to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.

biosimulators / Biosimulators

Submit Neuron 8.0.0 #373

Summary of tests

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (3.4 s)

docker_image.DeclaresSupportedEnvironmentVariables (0.3 s)

docker_image.HasBioContainersLabels (0.3 s)

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (11.8 s)

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)

published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)

published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

sedml.SimulatorProducesLinear3DPlots (0.8 s)

sedml.SimulatorProducesLogarithmic3DPlots (0.8 s)

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.8 s)

sedml.SimulatorSupportsAlgorithmParameters (0.8 s)

sedml.SimulatorSupportsComputeModelChanges (0.7 s)

sedml.SimulatorSupportsModelAttributeChanges (0.7 s)

sedml.SimulatorSupportsRepeatedTasksWithChanges (0.8 s)

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (0.7 s)

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (8.8 s)

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (8.6 s)

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (8.8 s)

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (8.6 s)

sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (8.7 s)

sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (9.4 s)

sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (9.3 s)

sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (8.6 s)

sedml.SimulatorSupportsSubstitutingAlgorithms (26.4 s)

Summary of tests

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (3.4 s)

docker_image.DeclaresSupportedEnvironmentVariables (0.3 s)

docker_image.HasBioContainersLabels (0.2 s)

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (11.7 s)

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)

published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

`cli.CliDescribesSupportedEnvironmentVariablesInline` (3.4 s)

`docker_image.DeclaresSupportedEnvironmentVariables` (0.3 s)

`docker_image.HasBioContainersLabels` (0.3 s)

`published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE` (11.8 s)

`published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells` (0.0 s)

`sedml.SimulatorProducesLinear3DPlots` (0.8 s)

`sedml.SimulatorProducesLogarithmic3DPlots` (0.8 s)

`sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges` (0.8 s)

`sedml.SimulatorSupportsAlgorithmParameters` (0.8 s)

`sedml.SimulatorSupportsComputeModelChanges` (0.7 s)

`sedml.SimulatorSupportsModelAttributeChanges` (0.7 s)

`sedml.SimulatorSupportsRepeatedTasksWithChanges` (0.8 s)

`sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables` (0.7 s)

`sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges` (8.8 s)

`sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges` (8.6 s)

`sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges` (8.8 s)

`sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks` (8.6 s)

`sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges` (8.7 s)

`sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks` (9.4 s)

`sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes` (9.3 s)

`sedml.SimulatorSupportsRepeatedTasksWithVectorRanges` (8.6 s)

`sedml.SimulatorSupportsSubstitutingAlgorithms` (26.4 s)

`cli.CliDescribesSupportedEnvironmentVariablesInline` (3.4 s)

`docker_image.DeclaresSupportedEnvironmentVariables` (0.3 s)

`docker_image.HasBioContainersLabels` (0.2 s)

`published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE` (11.7 s)

`published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl` (0.0 s)

`published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator` (0.0 s)

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